/*.................................................................................................................*/
public String getStringForTree(int ic) {
if (treesBlock == null) return "";
Tree tree = treesBlock.getTree(ic);
if (tree == null) return "";
if (tree.hasPolytomies(tree.getRoot())) return "Yes";
else return "No";
}
/*.................................................................................................................*/
public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) {
logln("Preparing to receive TNT trees.");
boolean success = false;
taxa = treeList.getTaxa();
// TODO finalScore.setValue(finalValue);
suppressProjectPanelReset();
CommandRecord oldCR = MesquiteThread.getCurrentCommandRecord();
CommandRecord scr = new CommandRecord(true);
MesquiteThread.setCurrentCommandRecord(scr);
// define file paths and set tree files as needed.
setFileNames();
String[] outputFilePaths = externalProcRunner.getOutputFilePaths();
String treeFilePath = outputFilePaths[OUT_TREEFILE];
taxonNumberTranslation = getTaxonNumberTranslation(taxa);
namer.setNumberTranslationTable(taxonNumberTranslation);
runFilesAvailable();
// read in the tree files
success = false;
Tree t = null;
MesquiteBoolean readSuccess = new MesquiteBoolean(false);
// TreeVector tv = new TreeVector(taxa);
if (bootstrapOrJackknife()) {
if (resamplingAllConsensusTrees)
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Rep",
0,
readSuccess,
false,
false,
null,
namer); // set first tree number as 0 as will remove the first one later.
else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Majority Rule Tree",
1,
readSuccess,
false,
false,
freqRef,
namer);
} else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNTTree",
1,
readSuccess,
false,
harvestOnlyStrictConsensus,
null,
namer);
success = t != null;
if (success && bootstrapOrJackknife() && resamplingAllConsensusTrees) {
t = t.cloneTree();
treeList.removeElementAt(0, false); // get rid of first one as this is the bootstrap tree
}
MesquiteThread.setCurrentCommandRecord(oldCR);
success = readSuccess.getValue();
if (!success) {
logln("Execution of TNT unsuccessful [2]");
if (!beanWritten) postBean("unsuccessful [2]", false);
beanWritten = true;
} else {
if (!beanWritten) postBean("successful", false);
beanWritten = true;
}
desuppressProjectPanelReset();
if (data != null) data.decrementEditInhibition();
// manager.deleteElement(tv); // get rid of temporary tree block
externalProcRunner.finalCleanup();
if (success) return t;
return null;
}
/*................................................................................................*/
private TreeVector fillBlock(Taxa taxa) { // TODO: fill in
TreeVector filledVector = new TreeVector(taxa);
int vectorTreeCount = 0;
for (int fillers = 0; fillers < fillerTasks.size(); fillers++) {
if (fillerTasks.get(fillers) instanceof SampleOneTreeFromFile) {
((SampleOneTreeFromFile) fillerTasks.get(fillers))
.resetTreesToSample(); // One unnecessary resetting of bits on first call
TreeVector tempTreeVector = new TreeVector(taxa);
((TreeBlockFiller) fillerTasks.get(fillers)).fillTreeBlock(tempTreeVector, 1);
if (tempTreeVector.getNumberOfTrees() < 1) {
logln(
"Not enough trees were supplied by "
+ ((TreeBlockFiller) fillerTasks.get(fillers)).getName()
+ "; "
+ tempTreeVector.getNumberOfTrees()
+ " provided, one requested.");
;
}
if (tempTreeVector.getNumberOfTrees() > 0) {
int treeCount = 0;
while (treeCount < 1
&& treeCount
< tempTreeVector
.getNumberOfTrees()) { // Check so we don't ask for more trees that are there.
filledVector.addElement(tempTreeVector.getTree(treeCount), false);
if (filledVector != null && tempTreeVector != null) {
if (filledVector.getTree(vectorTreeCount) != null
&& tempTreeVector.getName() != null) {
if (filledVector.getTree(vectorTreeCount).getName() != null)
logln(
filledVector.getTree(vectorTreeCount).getName()
+ " added from "
+ tempTreeVector.getName());
}
}
treeCount++;
vectorTreeCount++;
}
}
tempTreeVector.dispose(); // disposed to reduce memory demands
// (fillerTask.get(fillers)).
}
}
return filledVector;
}